Quantitative modelling of nutrient-limited growth of bacterial colonies in microfluidic cultivation

<p>Data for &quot;Quantitative modelling of nutrient-limited growth of bacterial colonies in microfluidic cultivation&quot;</p> <p>&nbsp;</p> <p>GrowthChannelExperiments contains the data-folders of the following growth channel experiments:<br> ***********************************************************************************************</p> <p>Name&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Feeding Concentration [in units of 0.195mM PCA]<br> nd004_series1&nbsp;&nbsp; &nbsp;0.5<br> nd004_series2&nbsp;&nbsp; &nbsp;0.5<br> nd004_series3&nbsp;&nbsp; &nbsp;0.5<br> nd004_series4&nbsp;&nbsp; &nbsp;2.0<br> nd004_series5&nbsp;&nbsp; &nbsp;2.0<br> nd004_series6&nbsp;&nbsp; &nbsp;2.0<br> nd004_series7&nbsp;&nbsp; &nbsp;3.0<br> nd004_series8&nbsp;&nbsp; &nbsp;3.0<br> nd112_series2&nbsp;&nbsp; &nbsp;0.25<br> nd112_series3&nbsp;&nbsp; &nbsp;0.25<br> nd112_series7&nbsp;&nbsp; &nbsp;3.0<br> nd112_series8&nbsp;&nbsp; &nbsp;3.0</p> <p>Every folder contains:<br> -&nbsp;&nbsp; &nbsp;a tif-file with captured image series<br> -&nbsp;&nbsp; &nbsp;a PIV*-folder with four PIV-files for every frame pair. The four files belong to intermediate results of the multistep PIV. The final PIV-result is given in the file step2*.dat.nmt.<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;The PIV result will be stored in a plain text file. Each line in this file correspond to each PIV vector and comprised of 16 columns:<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;x &nbsp;&nbsp; &nbsp;y &nbsp;&nbsp; &nbsp;ux1 &nbsp;&nbsp; &nbsp;uy1 &nbsp;&nbsp; &nbsp;mag1 &nbsp;&nbsp; &nbsp;ang1 &nbsp;&nbsp; &nbsp;p1&nbsp;&nbsp; &nbsp;ux2 &nbsp;&nbsp; &nbsp;uy2 &nbsp;&nbsp; &nbsp;mag2 &nbsp;&nbsp; &nbsp;ang2 &nbsp;&nbsp; &nbsp;p2 &nbsp;&nbsp; &nbsp;ux0 &nbsp;&nbsp; &nbsp;uy0 &nbsp;&nbsp; &nbsp;mag0 &nbsp;&nbsp; &nbsp;flag<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- (x,y) is the position of the vector (center of the interrogation window).<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- ux1, uy1 are the x and y component of the vector (displacement) obtained from the 1st correlation peak.<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- mag1 is the magnitude (norm) of the vector.<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- ang1, is the angle between the current vector and the vector interpolated from previous PIV iteration.<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- p1 is the correlation value of the 1st peak.<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- ux2,uy2,mag2,ang2,p2 are the values for the vector obtained from the 2nd correlation peak.<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- ux0, uy0, mag0 are the vector value at (x,y) interpolated from previous PIV iteration.<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- flag is a column used for mark whether this vector value is interpolated (marked as 999) or switched between 1st and 2nd peak (marked as 21), or invalid (-1).&nbsp;<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;According to the PIV-Fiji-plugin as provided by Qingzong Tseng, used also in :&nbsp;<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Tseng, Q. et al. Spatial organization of the extracellular matrix regulates cell-cell junction positioning. Proc. Natl. Acad. Sci. 109, 1506&ndash;1511 (2012)<br> -&nbsp;&nbsp; &nbsp;two traj*.dat files, belonging to particle positions of the corresponding simulation with monod/teissier uptake.&nbsp;<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Columns correspond to&nbsp;<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;1 : time | 2 : cellID | 3 : rx | 4 : ry | 5 : rz | 6: species | 7 : vx | 8 : vy | 9 : vz | 10 : fx | 11 : fy | 12 : fz | 13 : B(g) |<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- rx,ry,rz 3D coordinates of particle<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- species is either 0 (living cell) or 1 (wall-particle)<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- vx,vy,vz 3D velocity of particle<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- fx,fy,fz 3D force of particle<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- B(g) growth force constant dependent on local g-concentration<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Note that due to the simulation being 2D, rx=constant and vx=0=fx.<br> -&nbsp;&nbsp; &nbsp;two g*.dat files, belonging to nutrient concentrations of the corresponding simulation with monod/teissier uptake.&nbsp;<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Columns correspond to&nbsp;<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;1 : time | 2 : gridx | 3 : gridy | 4 : gridz | 5 : g-conc | 6: kcons | 7 : kprod | 8: Dlocal |<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- gridx,gridy,gridz coordinates of lattice side<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- kcons local nutrient consumption rate<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- kprod local nutrient production rate (always zero)<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;-- Dlocal local diffusion constant</p> <p>&nbsp;</p> <p>GrowthChamberExperiments contains the the data-folders of the following growth chamber experiments:<br> ***************************************************************************************************</p> <p>Name&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Feeding Concentration [in units of 0.195mM PCA]<br> nd143_xy009&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;1.0<br> nd143_xy013&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;1.0<br> nd143_xy025&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;1.0<br> nd143_xy032&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;1.0<br> nd143_xy059&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;1.0<br> nd143_xy060&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;1.0<br> nd143_xy061&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;1.0<br> nd143_xy165&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;0.1<br> nd143_xy184&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;0.1<br> nd143_xy214&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;0.1</p> <p>Every folder contains:<br> -&nbsp;&nbsp; &nbsp;a tif-file with captured image series<br> -&nbsp;&nbsp; &nbsp;five traj*.dat files, belonging to particle positions of the corresponding simulation with monod-uptake and five different ratios of the diffusion constants in- and outside the colony.<br> -&nbsp;&nbsp; &nbsp;five g*.dat files, belonging to nutrient concentrations of the corresponding simulation with monod-uptake and five different ratios of the diffusion constants in- and outside the colony.</p>